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Zhang Z, Ge M, Guo Q, Jiang Y, Jia W, Gao L, Hu J. Ultrahigh-Throughput Screening of High-β-Xylosidase-Producing Penicillium piceum and Investigation of the Novel β-Xylosidase Characteristics. J Fungi (Basel) 2022; 8:jof8040325. [PMID: 35448556 PMCID: PMC9024563 DOI: 10.3390/jof8040325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/07/2022] [Accepted: 03/16/2022] [Indexed: 02/04/2023] Open
Abstract
A droplet-based microfluidic ultrahigh-throughput screening technology has been developed for the selection of high-β-xylosidase-producing Penicillium piceum W6 from the atmospheric and room-temperature plasma-mutated library of P. piceum. β-xylosidase hyperproducers filamentous fungi, P. piceum W6, exhibited an increase in β-xylosidase activity by 7.1-fold. A novel β-D-xylosidase was purified from the extracellular proteins of P. piceum W6 and designated as PpBXL. The optimal pH and temperature of PpBXL were 4.0 and 70 °C, respectively. PpBXL had high stability an acidic pH range of 3.0-5.0 and exhibited good thermostability with a thermal denaturation half-life of 10 days at 70 °C. Moreover, PpBXL showed the bifunctional activities of α-L-arabinofuranosidase and β-xylosidase. Supplementation with low-dose PpBXL (100 μg/g substrate) improved the yields of glucose and xylose generated from delignified biomass by 36-45%. The synergism between PpBXL and lignocellulolytic enzymes enhanced delignified biomass saccharification, increased the Xyl/Ara ratio, and decreased the strength of hydrogen bonds.
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Affiliation(s)
- Zhaokun Zhang
- School of Chemical Engineering, Inner Mongolia University of Technology, Hohhot 010051, China;
| | - Mingyue Ge
- Tianjin Key Laboratory for Industrial BioSystems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, No. 32, Xiqi Road, Tianjin Airport Economic Park, Tianjin 300308, China; (M.G.); (Q.G.); (Y.J.); (W.J.)
| | - Qi Guo
- Tianjin Key Laboratory for Industrial BioSystems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, No. 32, Xiqi Road, Tianjin Airport Economic Park, Tianjin 300308, China; (M.G.); (Q.G.); (Y.J.); (W.J.)
| | - Yi Jiang
- Tianjin Key Laboratory for Industrial BioSystems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, No. 32, Xiqi Road, Tianjin Airport Economic Park, Tianjin 300308, China; (M.G.); (Q.G.); (Y.J.); (W.J.)
| | - Wendi Jia
- Tianjin Key Laboratory for Industrial BioSystems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, No. 32, Xiqi Road, Tianjin Airport Economic Park, Tianjin 300308, China; (M.G.); (Q.G.); (Y.J.); (W.J.)
| | - Le Gao
- Tianjin Key Laboratory for Industrial BioSystems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, No. 32, Xiqi Road, Tianjin Airport Economic Park, Tianjin 300308, China; (M.G.); (Q.G.); (Y.J.); (W.J.)
- Correspondence: (L.G.); (J.H.)
| | - Jianhua Hu
- School of Chemical Engineering, Inner Mongolia University of Technology, Hohhot 010051, China;
- Correspondence: (L.G.); (J.H.)
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Contributions and characteristics of two bifunctional GH43 β-xylosidase /α-L-arabinofuranosidases with different structures on the xylan degradation of Paenibacillus physcomitrellae strain XB. Microbiol Res 2021; 253:126886. [PMID: 34687975 DOI: 10.1016/j.micres.2021.126886] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/24/2021] [Accepted: 09/30/2021] [Indexed: 11/20/2022]
Abstract
Xylan is one of the major polymeric hemicellulosic constituents of lignocellulosic biomass, and its effective utilization by microorganisms is crucial for the economical production of biofuels. In this study, Paenibacillus physcomitrellae XB exhibited different xylan degradation ability on different substrates of corncob xylan (CCX), oat spelt xylan (OSX), wheat flour arabinoxylan (AX) and beech wood xylan (BWX). The RT-QPCR result showed that two genes (Pph_0602 and Pph_2344) belonging to the glycoside hydrolase family 43 were up-regulated more than 5-fold on CCX and xylose. Substrate-specific assays with purified proteins Ppxyl43A (Pph_0602) and Ppxyl43B (Pph_2344) revealed that both exhibited β-xylosidase activity toward the chromogenic substrate p-nitrophenyl-β-D-xylopyranoside, and α-L-arabinofuranosidase activity toward p-nitrophenyl-α-L-arabinofuranoside, indicating their bifunctionality. By testing their degradation characteristics on different natural substrates, it was found that both Ppxyl43A and Ppxyl43B showed similar degradation ability on CCX and OSX. Both enzymes could hydrolyze xylohexaose and xylobiose completely to xylose, but could not hydrolyze BWX and AX, suggesting they mainly hydrolyze xylo-oligosaccharides by β-xylosidase activity. Further analysis showed that both of them displayed very high pH stability and thermostability on the β-xylosidase activity, but Ppxy143B exhibited wider pH and temperature ranges, higher pH and temperature stability, was less influenced by metal ions, and had a slower start-up response than Ppxyl43A. Given their predicted structure, it is likely that the enzymatic differences between Ppxyl43A and Ppxyl43B might be related to the extra C-terminus domain (GH43_C2) in Ppxyl43B, which could enhance the enzymatic stability while restricting the substrates' or metal ions' access to the active sites of Ppxyl43B. In conclusion, both Ppxyl43A and Ppxyl43B were β-xylosidase/α-L-arabinofuranosidase bifunctional enzymes and might be useful in xylan biomass conversion, especially in the hydrolysis of xylo-oligosaccharides into xylose.
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3
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Stabel M, Hagemeister J, Heck Z, Aliyu H, Ochsenreither K. Characterization and Phylogenetic Analysis of a Novel GH43 β-Xylosidase From Neocallimastix californiae. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:692804. [PMID: 37744100 PMCID: PMC10512374 DOI: 10.3389/ffunb.2021.692804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/26/2021] [Indexed: 09/26/2023]
Abstract
Degradation of lignocellulosic materials to release fermentable mono- and disaccharides is a decisive step toward a sustainable bio-based economy, thereby increasing the demand of robust and highly active lignocellulolytic enzymes. Anaerobic fungi of the phylum Neocallimastigomycota are potent biomass degraders harboring a huge variety of such enzymes. Compared to cellulose, hemicellulose degradation has received much less attention; therefore, the focus of this study has been the enzymatic xylan degradation of anaerobic fungi as these organisms produce some of the most effective known hydrolytic enzymes. We report the heterologous expression of a GH43 xylosidase, Xyl43Nc, and a GH11 endoxylanase, X11Nc, from the anaerobic fungus Neocallimastix californiae in Escherichia coli. The enzymes were identified by screening of the putative proteome. Xyl43Nc was highly active against 4-Nitrophenol-xylopyranosides with a Km of 0.72 mM, a kcat of 29.28 s-1, a temperature optimum of 32°C and a pH optimum of 6. When combined, Xyl43Nc and X11Nc released xylose from beechwood xylan and arabinoxylan from wheat. Phylogenetic analysis revealed that Xyl43Nc shares common ancestry with enzymes from Spirochaetes and groups separately from Ascomycete sequences in our phylogeny, highlighting the importance of horizontal gene transfer in the evolution of the anaerobic fungi.
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Affiliation(s)
- Marcus Stabel
- Process Engineering in Life Sciences 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
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4
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Morais MAB, Coines J, Domingues MN, Pirolla RAS, Tonoli CCC, Santos CR, Correa JBL, Gozzo FC, Rovira C, Murakami MT. Two distinct catalytic pathways for GH43 xylanolytic enzymes unveiled by X-ray and QM/MM simulations. Nat Commun 2021; 12:367. [PMID: 33446650 PMCID: PMC7809346 DOI: 10.1038/s41467-020-20620-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023] Open
Abstract
Xylanolytic enzymes from glycoside hydrolase family 43 (GH43) are involved in the breakdown of hemicellulose, the second most abundant carbohydrate in plants. Here, we kinetically and mechanistically describe the non-reducing-end xylose-releasing exo-oligoxylanase activity and report the crystal structure of a native GH43 Michaelis complex with its substrate prior to hydrolysis. Two distinct calcium-stabilized conformations of the active site xylosyl unit are found, suggesting two alternative catalytic routes. These results are confirmed by QM/MM simulations that unveil the complete hydrolysis mechanism and identify two possible reaction pathways, involving different transition state conformations for the cleavage of xylooligosaccharides. Such catalytic conformational promiscuity in glycosidases is related to the open architecture of the active site and thus might be extended to other exo-acting enzymes. These findings expand the current general model of catalytic mechanism of glycosidases, a main reaction in nature, and impact on our understanding about their interaction with substrates and inhibitors.
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Affiliation(s)
- Mariana A B Morais
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
- Departament de Química Inorgànica i Orgànica & Institut de Química Teórica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, 08028, Spain
| | - Joan Coines
- Departament de Química Inorgànica i Orgànica & Institut de Química Teórica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, 08028, Spain
| | - Mariane N Domingues
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Renan A S Pirolla
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Celisa C C Tonoli
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Camila R Santos
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Jessica B L Correa
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Fabio C Gozzo
- Dalton Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, Campinas, 13083-970, Brazil
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & Institut de Química Teórica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, 08028, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08010, Spain.
| | - Mario T Murakami
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil.
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β-Xylosidases: Structural Diversity, Catalytic Mechanism, and Inhibition by Monosaccharides. Int J Mol Sci 2019; 20:ijms20225524. [PMID: 31698702 PMCID: PMC6887791 DOI: 10.3390/ijms20225524] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/02/2019] [Accepted: 11/04/2019] [Indexed: 12/20/2022] Open
Abstract
Xylan, a prominent component of cellulosic biomass, has a high potential for degradation into reducing sugars, and subsequent conversion into bioethanol. This process requires a range of xylanolytic enzymes. Among them, β-xylosidases are crucial, because they hydrolyze more glycosidic bonds than any of the other xylanolytic enzymes. They also enhance the efficiency of the process by degrading xylooligosaccharides, which are potent inhibitors of other hemicellulose-/xylan-converting enzymes. On the other hand, the β-xylosidase itself is also inhibited by monosaccharides that may be generated in high concentrations during the saccharification process. Structurally, β-xylosidases are diverse enzymes with different substrate specificities and enzyme mechanisms. Here, we review the structural diversity and catalytic mechanisms of β-xylosidases, and discuss their inhibition by monosaccharides.
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6
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Zhou A, Hu Y, Li J, Wang W, Zhang M, Guan S. Characterization of a recombinant β-xylosidase of GH43 family fromBacteroides ovatusstrain ATCC 8483. BIOCATAL BIOTRANSFOR 2019. [DOI: 10.1080/10242422.2019.1631813] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Andong Zhou
- School of Life Sciences, Jilin University, Changchun, P. R. China
| | - Yanbo Hu
- School of Life Sciences, Northeast Normal University, Changchun, P. R. China
| | - Jingjing Li
- Beijing Institute of Metrology, Beijing, P. R. China
| | - Weiyang Wang
- School of Life Sciences, Northeast Normal University, Changchun, P. R. China
| | - Mengshan Zhang
- School of Life Sciences, Northeast Normal University, Changchun, P. R. China
| | - Shuwen Guan
- School of Life Sciences, Jilin University, Changchun, P. R. China
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The modular arabinanolytic enzyme Abf43A-Abf43B-Abf43C from Ruminiclostridium josui consists of three GH43 modules classified in different subfamilies. Enzyme Microb Technol 2019; 124:23-31. [PMID: 30797476 DOI: 10.1016/j.enzmictec.2019.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 01/18/2019] [Accepted: 01/29/2019] [Indexed: 11/20/2022]
Abstract
The abnA gene from Ruminiclostridium josui encodes the large modular arabinanolytic enzyme, Abf43A-Abf43B-Abf43C, consisting of an N-terminal signal peptide, a Laminin_G_3 module, a GH43_22 module, a Laminin_G_3 module, a Big_4 module, a GH43_26 module, a GH43_34 module and a dockerin module in order with a calculated molecular weight of 204,108. Three truncated enzymes were recombinantly produced in Escherichia coli and biochemically characterized, RjAbf43A consisting of the first Laminin_G_3 module and GH43_22 module, RjAbf43B consisting of the second Laminin_G_3 module, Big_4 module and GH43_26 module, and RjAbf43C consisting of the GH43_34 module. RjAbf43A showed a strong α-l-arabinofuranosidase activity toward sugar beet arabinan, highly branched arabinan but not linear arabinan, thus it acted in the removal of arabinose side chains from sugar beet arabinan. By contrast, RjAbf43B showed a strong exo-α-1,5-l-arabinofuranosidase activity toward linear arabinan and arabinooligosaccharides whereas RjAbf43C showed low activity toward these substrates. Although RjAbf43B was activated by the presence of some metal ions such as Zn2+, Mg2+ and Ni2+, RjAbf43A was inhibited by these ions. RjAbf43A and RjAbf43B attacked sugar beet arabinan in a synergistic manner. By comparison, RjAbf43A-Abf43B containing both GH43_22 and GH43_26 modules showed lower hydrolytic activity toward sugar beet arabinan but higher activity toward sugar beet fiber than the sum of the individual activities of RjAbf43A and RjAbf43B, suggesting that the coexistence of two distinct GH43 modules in a single polypeptide is important for the efficient hydrolysis of an insoluble and natural polysaccharide but not a soluble substrate.
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8
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EcXyl43 β-xylosidase: molecular modeling, activity on natural and artificial substrates, and synergism with endoxylanases for lignocellulose deconstruction. Appl Microbiol Biotechnol 2018; 102:6959-6971. [PMID: 29876606 DOI: 10.1007/s00253-018-9138-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/10/2018] [Accepted: 05/15/2018] [Indexed: 10/14/2022]
Abstract
Biomass hydrolysis constitutes a bottleneck for the biotransformation of lignocellulosic residues into bioethanol and high-value products. The efficient deconstruction of polysaccharides to fermentable sugars requires multiple enzymes acting concertedly. GH43 β-xylosidases are among the most interesting enzymes involved in hemicellulose deconstruction into xylose. In this work, the structural and functional properties of β-xylosidase EcXyl43 from Enterobacter sp. were thoroughly characterized. Molecular modeling suggested a 3D structure formed by a conserved N-terminal catalytic domain linked to an ancillary C-terminal domain. Both domains resulted essential for enzymatic activity, and the role of critical residues, from the catalytic and the ancillary modules, was confirmed by mutagenesis. EcXyl43 presented β-xylosidase activity towards natural and artificial substrates while arabinofuranosidase activity was only detected on nitrophenyl α-L-arabinofuranoside (pNPA). It hydrolyzed xylobiose and purified xylooligosaccharides (XOS), up to degree of polymerization 6, with higher activity towards longer XOS. Low levels of activity on commercial xylan were also observed, mainly on the soluble fraction. The addition of EcXyl43 to GH10 and GH11 endoxylanases increased the release of xylose from xylan and pre-treated wheat straw. Additionally, EcXyl43 exhibited high efficiency and thermal stability under its optimal conditions (40 °C, pH 6.5), with a half-life of 58 h. Therefore, this enzyme could be a suitable additive for hemicellulases in long-term hydrolysis reactions. Because of its moderate inhibition by monomeric sugars but its high inhibition by ethanol, EcXyl43 could be particularly more useful in separate hydrolysis and fermentation (SHF) than in simultaneous saccharification and co-fermentation (SSCF) or consolidated bioprocessing (CBP).
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Identification and characterization of the first β-1,3-d-xylosidase from a gram-positive bacterium, Streptomyces sp. SWU10. Enzyme Microb Technol 2017; 112:72-78. [PMID: 29499784 DOI: 10.1016/j.enzmictec.2017.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 11/21/2022]
Abstract
In previous reports, we characterized four endo-xylanases produced by Streptomyces sp. strain SWU10 that degrade xylans to several xylooligosaccharides. To obtain a set of enzymes to achieve complete xylan degradation, a β-d-xylosidase gene was cloned and expressed in Escherichia coli, and the recombinant protein, named rSWU43A, was characterized. SWU43A is composed of 522 amino acids and does not contain a signal peptide, indicating that the enzyme is an intracellular protein. SWU43A was revealed to contain a Glyco_hydro_43 domain and possess the three conserved amino acid residues of the glycoside hydrolase family 43 proteins. The molecular mass of rSWU43A purified by Ni-affinity column chromatography was estimated to be 60kDa. The optimum reaction conditions of rSWU43A were pH 6.5 and 40°C. The enzyme was stable up to 40°C over a wide pH range (3.1-8.9). rSWU43A activity was enhanced by Fe2+ and Mn2+ and inhibited by various metals (Ag+, Cd2+, Co2+, Cu2+, Hg2+, Ni2+, and Zn2+), d-xylose, and l-arabinose. rSWU43A showed activity on p-nitrophenyl-β-d-xylopyranoside and p-nitrophenyl-α-l-arabinofuranoside substrates, with specific activities of 0.09 and 0.06U/mg, respectively, but not on any xylosidic or arabinosidic polymers. rSWU43A efficiently degraded β-1,3-xylooligosaccharides to produce xylose but showed little activity towards β-1,4-xylobiose, with specific activities of 1.33 and 0.003U/mg, respectively. These results demonstrate that SWU43A is a β-1,3-d-xylosidase (EC 3.2.1.72), which to date has only been described in the marine bacterium Vibrio sp. Therefore, rSWU43A of Streptomyces sp. is the first β-1,3-xylosidase found in gram-positive bacteria. SWU43A could be useful as a specific tool for the structural elucidation and production of xylose from β-1,3-xylan in seaweed cell walls.
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10
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Matsuzawa T, Kaneko S, Kishine N, Fujimoto Z, Yaoi K. Crystal structure of metagenomic β-xylosidase/ α-l-arabinofuranosidase activated by calcium. J Biochem 2017; 162:173-181. [PMID: 28204531 DOI: 10.1093/jb/mvx012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 01/26/2017] [Indexed: 11/13/2022] Open
Abstract
The crystal structure of metagenomic β-xylosidase/α-l-arabinofuranosidase CoXyl43, activated by calcium ions, was determined in its apo and complexed forms with xylotriose or l-arabinose in the presence and absence of calcium. The presence of calcium ions dramatically increases the kcat of CoXyl43 for p-nitrophenyl β-d-xylopyranoside and reduces the Michaelis constant for p-nitrophenyl α-l-arabinofuranoside. CoXyl43 consists of a single catalytic domain comprised of a five-bladed β-propeller. In the presence of calcium, a single calcium ion was observed at the centre of this catalytic domain, behind the catalytic pocket. In the absence of calcium, the calcium ion was replaced with one sodium ion and one water molecule, and the positions of these cations were shifted by 1.3 Å. The histidine-319 side chain, which coordinates to the 2-hydroxyl oxygen atom of the bound xylose molecule in the catalytic pocket, also coordinates to the calcium ion, but not to the sodium ion. The calcium-dependent increase in activity appears to be caused by the structural change in the catalytic pocket induced by the tightly bound calcium ion and coordinating water molecules, and by the protonation state of glutamic acid-268, the catalytic acid of the enzyme. Our findings further elucidate the complex relationship between metal ions and glycosidases.
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Affiliation(s)
- Tomohiko Matsuzawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Satoshi Kaneko
- Department of Subtropical Biochemistry and Biotechnology Faculty of Agriculture, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Naomi Kishine
- Advanced Analysis Center, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Zui Fujimoto
- Advanced Analysis Center, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Katsuro Yaoi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
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11
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Production and Characteristics of a Novel Xylose- and Alkali-tolerant GH 43 β-xylosidase from Penicillium oxalicum for Promoting Hemicellulose Degradation. Sci Rep 2017; 7:11600. [PMID: 28912429 PMCID: PMC5599605 DOI: 10.1038/s41598-017-11573-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 08/23/2017] [Indexed: 11/09/2022] Open
Abstract
β-xylosidase is a pivotal enzyme for complete degradation of xylan in hemicelluloses of lignocelluloses, and the xylose- and alkali-tolerant β-xylosidase with high catalytic activity is very attractive for promoting enzymatic hydrolysis of alkaline-pretreated lignocellulose. In this study, a novel intracellular glycoside hydrolase family 43 β-xylosidase gene (xyl43) from Penicillium oxalicum 114-2 was successfully high-level overexpressed in Pichia pastoris, and the secreted enzyme was characterized. The β-xylosidase Xyl43 exhibited great pH stability and high catalytic activity in the range of pH 6.0 to 8.0, and high tolerance to xylose with the Ki value of 28.09 mM. The Xyl43 could effectively promote enzymatic degradation of different source of xylan and hemicellulose contained in alkaline-pretreated corn stover, and high conversion of xylan to xylose could be obtained.
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12
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Mechelke M, Koeck DE, Broeker J, Roessler B, Krabichler F, Schwarz WH, Zverlov VV, Liebl W. Characterization of the arabinoxylan-degrading machinery of the thermophilic bacterium Herbinix hemicellulosilytica-Six new xylanases, three arabinofuranosidases and one xylosidase. J Biotechnol 2017; 257:122-130. [PMID: 28450260 DOI: 10.1016/j.jbiotec.2017.04.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 04/20/2017] [Accepted: 04/20/2017] [Indexed: 10/19/2022]
Abstract
Herbinix hemicellulosilytica is a newly isolated, gram-positive, anaerobic bacterium with extensive hemicellulose-degrading capabilities obtained from a thermophilic biogas reactor. In order to exploit its potential as a source for new industrial arabinoxylan-degrading enzymes, six new thermophilic xylanases, four from glycoside hydrolase family 10 (GH10) and two from GH11, three arabinofuranosidases (1x GH43, 2x GH51) and one β-xylosidase (GH43) were selected. The recombinantly produced enzymes were purified and characterized. All enzymes were active on different xylan-based polysaccharides and most of them showed temperature-vs-activity profiles with maxima around 55-65°C. HPAEC-PAD analysis of the hydrolysates of wheat arabinoxylan and of various purified xylooligosaccharides (XOS) and arabinoxylooligosaccharides (AXOS) was used to investigate their substrate and product specificities: among the GH10 xylanases, XynB showed a different product pattern when hydrolysing AXOS compared to XynA, XynC, and XynD. None of the GH11 xylanases was able to degrade any of the tested AXOS. All three arabinofuranosidases, ArfA, ArfB and ArfC, were classified as type AXH-m,d enzymes. None of the arabinofuranosidases was able to degrade the double-arabinosylated xylooligosaccharides XA2+3XX. β-Xylosidase XylA (GH43) was able to degrade unsubstituted XOS, but showed limited activity to degrade AXOS.
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Affiliation(s)
- M Mechelke
- Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - D E Koeck
- Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - J Broeker
- Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - B Roessler
- Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - F Krabichler
- Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - W H Schwarz
- Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - V V Zverlov
- Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany; Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, 123182 Moscow Russia
| | - W Liebl
- Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany.
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13
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Jordan DB, Stoller JR, Lee CC, Chan VJ, Wagschal K. Biochemical Characterization of a GH43 β-Xylosidase from Bacteroides ovatus. Appl Biochem Biotechnol 2016; 182:250-260. [PMID: 27854035 DOI: 10.1007/s12010-016-2324-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 11/03/2016] [Indexed: 01/25/2023]
Abstract
Divalent metal-activated glycoside hydrolase family 43 (GH43) β-xylosidases have been found to have high k cat/K m for xylooligosaccharides and may demonstrate high efficacy in industrial reactors digesting hemicellulose. By searching an amino acid database, we found a Bacteroides ovatus GH43 β-xylosidase termed BoXA that is 81% identical in overall amino acid sequence to a GH43, divalent metal-activated β-xylosidase with high k cat/K m, and also it has 19 of 20 residues in the active site conserved. However, unlike its metal-activated homolog, the B. ovatus enzyme does not lose activity after extensive EDTA treatment nor does it gain activity by addition of divalent metal ions. Thus, either it cannot be activated by divalent metal or it maintains a tightly bound, non-exchangeable metal ion. At 25 °C and pH 6.0, the k cat is 69 s-1 for xylobiose and k cat/K m is 210 s-1 mM-1 for xylotriose, with the latter being 0.7 that of the highest known value. The determined K i for D-glucose is 4.9 M, which is the highest known for a β-xylosidase. The enzyme has potential utility operating in bioreactors digesting plant biomass.
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Affiliation(s)
- Douglas B Jordan
- USDA-ARS-National Center for Agricultural Utilization Research, Peoria, IL, 61604, USA.
| | - J Rose Stoller
- USDA-ARS-National Center for Agricultural Utilization Research, Peoria, IL, 61604, USA
| | - Charles C Lee
- USDA-ARS-Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Victor J Chan
- USDA-ARS-Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Kurt Wagschal
- USDA-ARS-Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
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14
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Hemsworth GR, Thompson AJ, Stepper J, Sobala ŁF, Coyle T, Larsbrink J, Spadiut O, Goddard-Borger ED, Stubbs KA, Brumer H, Davies GJ. Structural dissection of a complex Bacteroides ovatus gene locus conferring xyloglucan metabolism in the human gut. Open Biol 2016; 6:160142. [PMID: 27466444 PMCID: PMC4967831 DOI: 10.1098/rsob.160142] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/01/2016] [Indexed: 12/22/2022] Open
Abstract
The human gastrointestinal tract harbours myriad bacterial species, collectively termed the microbiota, that strongly influence human health. Symbiotic members of our microbiota play a pivotal role in the digestion of complex carbohydrates that are otherwise recalcitrant to assimilation. Indeed, the intrinsic human polysaccharide-degrading enzyme repertoire is limited to various starch-based substrates; more complex polysaccharides demand microbial degradation. Select Bacteroidetes are responsible for the degradation of the ubiquitous vegetable xyloglucans (XyGs), through the concerted action of cohorts of enzymes and glycan-binding proteins encoded by specific xyloglucan utilization loci (XyGULs). Extending recent (meta)genomic, transcriptomic and biochemical analyses, significant questions remain regarding the structural biology of the molecular machinery required for XyG saccharification. Here, we reveal the three-dimensional structures of an α-xylosidase, a β-glucosidase, and two α-l-arabinofuranosidases from the Bacteroides ovatus XyGUL. Aided by bespoke ligand synthesis, our analyses highlight key adaptations in these enzymes that confer individual specificity for xyloglucan side chains and dictate concerted, stepwise disassembly of xyloglucan oligosaccharides. In harness with our recent structural characterization of the vanguard endo-xyloglucanse and cell-surface glycan-binding proteins, the present analysis provides a near-complete structural view of xyloglucan recognition and catalysis by XyGUL proteins.
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Affiliation(s)
- Glyn R Hemsworth
- Department of Chemistry, York Structural Biology Laboratory, The University of York, Heslington, York YO10 5DD, UK
| | - Andrew J Thompson
- Department of Chemistry, York Structural Biology Laboratory, The University of York, Heslington, York YO10 5DD, UK
| | - Judith Stepper
- Department of Chemistry, York Structural Biology Laboratory, The University of York, Heslington, York YO10 5DD, UK
| | - Łukasz F Sobala
- Department of Chemistry, York Structural Biology Laboratory, The University of York, Heslington, York YO10 5DD, UK
| | - Travis Coyle
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Johan Larsbrink
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden Michael Smith Laboratories and Department of Chemistry, University of British Columbia, 2185 East Mall, Vancouver, British Columbia, Canada V6T 1Z4
| | - Oliver Spadiut
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden Wallenberg Wood Science Center, Royal Institute of Technology (KTH), Teknikringen 56-58, 100 44 Stockholm, Sweden
| | - Ethan D Goddard-Borger
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville Victoria 3052, Australia
| | - Keith A Stubbs
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Harry Brumer
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden Michael Smith Laboratories and Department of Chemistry, University of British Columbia, 2185 East Mall, Vancouver, British Columbia, Canada V6T 1Z4
| | - Gideon J Davies
- Department of Chemistry, York Structural Biology Laboratory, The University of York, Heslington, York YO10 5DD, UK
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15
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Jordan DB, Braker JD, Wagschal K, Stoller JR, Lee CC. Isolation and divalent-metal activation of a β-xylosidase, RUM630-BX. Enzyme Microb Technol 2016; 82:158-163. [DOI: 10.1016/j.enzmictec.2015.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 10/01/2015] [Accepted: 10/03/2015] [Indexed: 11/25/2022]
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16
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Jordan DB, Braker JD, Wagschal K, Lee CC, Chan VJ, Dubrovska I, Anderson S, Wawrzak Z. X-ray Crystal Structure of Divalent Metal-Activated β-xylosidase, RS223BX. Appl Biochem Biotechnol 2015. [DOI: 10.1007/s12010-015-1767-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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17
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Matsuzawa T, Kaneko S, Yaoi K. Screening, identification, and characterization of a GH43 family β-xylosidase/α-arabinofuranosidase from a compost microbial metagenome. Appl Microbiol Biotechnol 2015; 99:8943-54. [DOI: 10.1007/s00253-015-6647-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/09/2015] [Accepted: 04/19/2015] [Indexed: 01/09/2023]
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18
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Kaur AP, Nocek BP, Xu X, Lowden MJ, Leyva JF, Stogios PJ, Cui H, Di Leo R, Powlowski J, Tsang A, Savchenko A. Functional and structural diversity in GH62 α-L-arabinofuranosidases from the thermophilic fungus Scytalidium thermophilum. Microb Biotechnol 2014; 8:419-33. [PMID: 25267315 PMCID: PMC4408175 DOI: 10.1111/1751-7915.12168] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 08/16/2014] [Indexed: 01/22/2023] Open
Abstract
The genome of the thermophilic fungus Scytalidium thermophilum (strain CBS 625.91) harbours a wide range of genes involved in carbohydrate degradation, including three genes, abf62A, abf62B and abf62C, predicted to encode glycoside hydrolase family 62 (GH62) enzymes. Transcriptome analysis showed that only abf62A and abf62C are actively expressed during growth on diverse substrates including straws from barley, alfalfa, triticale and canola. The abf62A and abf62C genes were expressed in Escherichia coli and the resulting recombinant proteins were characterized. Calcium-free crystal structures of Abf62C in apo and xylotriose bound forms were determined to 1.23 and 1.48 Å resolution respectively. Site-directed mutagenesis confirmed Asp55, Asp171 and Glu230 as catalytic triad residues, and revealed the critical role of non-catalytic residues Asp194, Trp229 and Tyr338 in positioning the scissile α-L-arabinofuranoside bond at the catalytic site. Further, the +2R substrate-binding site residues Tyr168 and Asn339, as well as the +2NR residue Tyr226, are involved in accommodating long-chain xylan polymers. Overall, our structural and functional analysis highlights characteristic differences between Abf62A and Abf62C, which represent divergent subgroups in the GH62 family.
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Affiliation(s)
- Amrit Pal Kaur
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, M5S 3E5, Canada
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19
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Klippel B, Sahm K, Basner A, Wiebusch S, John P, Lorenz U, Peters A, Abe F, Takahashi K, Kaiser O, Goesmann A, Jaenicke S, Grote R, Horikoshi K, Antranikian G. Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria. Extremophiles 2014; 18:853-63. [PMID: 25108363 DOI: 10.1007/s00792-014-0676-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/08/2014] [Indexed: 10/24/2022]
Abstract
Subseafloor sediment samples derived from a sediment core of 60 m length were used to enrich psychrophilic aerobic bacteria on cellulose, xylan, chitin, and starch. A variety of species belonging to Alpha- and Gammaproteobacteria and to Flavobacteria were isolated from sediment depths between 12 and 42 mbsf. Metagenomic DNA purified from the pooled enrichments was sequenced and analyzed for phylogenetic composition and presence of genes encoding carbohydrate-active enzymes. More than 200 open reading frames coding for glycoside hydrolases were identified, and more than 60 of them relevant for enzymatic degradation of lignocellulose. Four genes encoding β-glucosidases with less than 52% identities to characterized enzymes were chosen for recombinant expression in Escherichia coli. In addition one endomannanase, two endoxylanases, and three β-xylosidases were produced recombinantly. All genes could be actively expressed. Functional analysis revealed discrepancies and additional variability for the recombinant enzymes as compared to the sequence-based predictions.
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Affiliation(s)
- Barbara Klippel
- Institute of Technical Microbiology, Hamburg University of Technology, Kasernenstr. 12, 21073, Hamburg, Germany
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20
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McVey CE, Ferreira MJ, Correia B, Lahiri S, de Sanctis D, Carrondo MA, Lindley PF, de Sá Nogueira I, Soares CM, Bento I. The importance of the Abn2 calcium cluster in the endo-1,5-arabinanase activity from Bacillus subtilis. J Biol Inorg Chem 2014; 19:505-13. [PMID: 24549757 DOI: 10.1007/s00775-014-1105-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 12/18/2013] [Indexed: 10/25/2022]
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21
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Jordan DB, Vermillion KE, Grigorescu AA, Braker JD. Rehabilitation of faulty kinetic determinations and misassigned glycoside hydrolase family of retaining mechanism β-xylosidases. Arch Biochem Biophys 2013; 537:176-84. [PMID: 23916587 DOI: 10.1016/j.abb.2013.07.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 07/19/2013] [Accepted: 07/22/2013] [Indexed: 11/16/2022]
Abstract
We obtained Cx1 from a commercial supplier, whose catalog listed it as a β-xylosidase of glycoside hydrolase family 43. NMR experiments indicate retention of anomeric configuration in its reaction stereochemistry, opposing the assignment of GH43, which follows an inverting mechanism. Partial protein sequencing indicates Cx1 is similar to but not identical to β-xylosidases of GH52, including Q09LZ0, that have retaining mechanisms. Q09LZ0 β-xylosidase had been characterized biochemically in kinetic reactions that contained Tris. We overproduced Q09LZ0 and demonstrated that Tris is a competitive inhibitor of the β-xylosidase. Also, the previous work used grossly incorrect extinction coefficients for product 4-nitrophenol. We redetermined kinetic parameters using reactions that omitted Tris and using correct extinction coefficients for 4-nitrophenol. Cx1 and Q09LZ0 β-xylosidases were thus shown to possess similar kinetic properties when acting on 4-nitrophenyl-β-d-xylopyranoside and xylobiose. kcat pH profiles of Cx1 and Q09LZ0 acting on 4-nitrophenyl-β-d-xylopyranoside and xylobiose have patterns containing two rate increases with increasing acidity, not reported before for glycoside hydrolases. The dexylosylation step of 4-nitrophenyl-β-d-xylopyranoside hydrolysis mediated by Q09LZ0 is not rate determining for kcat(4NPX).
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Affiliation(s)
- Douglas B Jordan
- USDA-ARS-National Center for Agricultural Utilization Research, Peoria, IL 61604, USA.
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22
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Ahmed S, Luis AS, Bras JLA, Ghosh A, Gautam S, Gupta MN, Fontes CMGA, Goyal A. A novel α-L-arabinofuranosidase of family 43 glycoside hydrolase (Ct43Araf) from Clostridium thermocellum. PLoS One 2013; 8:e73575. [PMID: 24039988 PMCID: PMC3767815 DOI: 10.1371/journal.pone.0073575] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 07/27/2013] [Indexed: 11/25/2022] Open
Abstract
The study describes a comparative analysis of biochemical, structural and functional properties of two recombinant derivatives from Clostridium thermocellum ATCC 27405 belonging to family 43 glycoside hydrolase. The family 43 glycoside hydrolase encoding α-L-arabinofuranosidase (Ct43Araf) displayed an N-terminal catalytic module CtGH43 (903 bp) followed by two carbohydrate binding modules CtCBM6A (405 bp) and CtCBM6B (402 bp) towards the C-terminal. Ct43Araf and its truncated derivative CtGH43 were cloned in pET-vectors, expressed in Escherichia coli and functionally characterized. The recombinant proteins displayed molecular sizes of 63 kDa (Ct43Araf) and 34 kDa (CtGH43) on SDS-PAGE analysis. Ct43Araf and CtGH43 showed optimal enzyme activities at pH 5.7 and 5.4 and the optimal temperature for both was 50°C. Ct43Araf and CtGH43 showed maximum activity with rye arabinoxylan 4.7 Umg(-1) and 5.0 Umg(-1), respectively, which increased by more than 2-fold in presence of Ca(2+) and Mg(2+) salts. This indicated that the presence of CBMs (CtCBM6A and CtCBM6B) did not have any effect on the enzyme activity. The thin layer chromatography and high pressure anion exchange chromatography analysis of Ct43Araf hydrolysed arabinoxylans (rye and wheat) and oat spelt xylan confirmed the release of L-arabinose. This is the first report of α-L-arabinofuranosidase from C. thermocellum having the capacity to degrade both p-nitrophenol-α-L-arabinofuranoside and p-nitrophenol-α-L-arabinopyranoside. The protein melting curves of Ct43Araf and CtGH43 demonstrated that CtGH43 and CBMs melt independently. The presence of Ca(2+) ions imparted thermal stability to both the enzymes. The circular dichroism analysis of CtGH43 showed 48% β-sheets, 49% random coils but only 3% α-helices.
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Affiliation(s)
- Shadab Ahmed
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Ana Sofia Luis
- CIISA-Faculdade de MedicinaVeterinaria, Avenida da Universidade Técnica, Lisbon, Portugal
| | - Joana L. A. Bras
- CIISA-Faculdade de MedicinaVeterinaria, Avenida da Universidade Técnica, Lisbon, Portugal
| | - Arabinda Ghosh
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Saurabh Gautam
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Munishwar N. Gupta
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Carlos M. G. A. Fontes
- CIISA-Faculdade de MedicinaVeterinaria, Avenida da Universidade Técnica, Lisbon, Portugal
| | - Arun Goyal
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, India
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Arabinoxylan oligosaccharide hydrolysis by family 43 and 51 glycosidases from Lactobacillus brevis DSM 20054. Appl Environ Microbiol 2013; 79:6747-54. [PMID: 23995921 DOI: 10.1128/aem.02130-13] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Due to their potential prebiotic properties, arabinoxylan-derived oligosaccharides [(A)XOS] are of great interest as functional food and feed ingredients. While the (A)XOS metabolism of Bifidobacteriaceae has been extensively studied, information regarding lactic acid bacteria (LAB) is still limited in this context. The aim of the present study was to fill this important gap by characterizing candidate (A)XOS hydrolyzing glycoside hydrolases (GHs) identified in the genome of Lactobacillus brevis DSM 20054. Two putative GH family 43 xylosidases (XynB1 and XynB2) and a GH family 43 arabinofuranosidase (Abf3) were heterologously expressed and characterized. While the function of XynB1 remains unclear, XynB2 could efficiently hydrolyze xylooligosaccharides. Abf3 displayed high specific activity for arabinobiose but could not release arabinose from an (A)XOS preparation. However, two previously reported GH 51 arabinofuranosidases from Lb. brevis were able to specifically remove α-1,3-linked arabinofuranosyl residues from arabino-xylooligosaccharides (AXHm3 specificity). These results imply that Lb. brevis is at least genetically equipped with functional enzymes in order to hydrolyze the depolymerization products of (arabino)xylans and arabinans. The distribution of related genes in Lactobacillales genomes indicates that GH 43 and, especially, GH 51 glycosidase genes are rare among LAB and mainly occur in obligately heterofermentative Lactobacillus spp., Pediococcus spp., members of the Leuconostoc/Weissella branch, and Enterococcus spp. Apart from the prebiotic viewpoint, this information also adds new perspectives on the carbohydrate (i.e., pentose-oligomer) metabolism of LAB species involved in the fermentation of hemicellulose-containing substrates.
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Jordan DB, Lee CC, Wagschal K, Braker JD. Activation of a GH43 β-xylosidase by divalent metal cations: slow binding of divalent metal and high substrate specificity. Arch Biochem Biophys 2013; 533:79-87. [PMID: 23500142 DOI: 10.1016/j.abb.2013.02.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 02/26/2013] [Accepted: 02/27/2013] [Indexed: 11/19/2022]
Abstract
RS223-BX of glycoside hydrolase family 43 is a β-d-xylosidase that is strongly activated (k(cat)/K(m) as much as 116-fold) by the addition of divalent metal cations, Ca(2+), Co(2+), Fe(2+), Mg(2+), Mn(2+) and Ni(2+). Slow activation by Mg(2+) was demonstrated (k(on) 0.013 s(-1) mM(-1), k(off) 0.008 s(-1)) at pH 7.0 and 25 °C. k(off) and k(on) values are independent of Mg(2+) concentration, but k(off) and k(on) are slower in the presence of increasing levels of substrate 4-nitrophenyl-β-D-xylopyranoside. The kinetics strongly suggest that M(2+) binds to the enzyme rapidly, forming E M(2+), followed by slow isomerization to the activated enzyme, E* M(2+). Moderately high values of kcat (7-30 s(-1)) were found for M(2+)-activated RS223-BX acting on xylobiose (natural substrate) at pH 7.0 and 25 °C. Certain M(2+)-activated RS223-BX exhibit the highest reported values of k(cat)/K(m) of any β-xylosidase acting on natural substrates: for example, at pH 7.0 and 25°C, xylobiose (Mn(2+), 190 s(-1) mM(-1)), xylotriose (Ca(2+), 150 s(-1) mM(-1)) and xylotetraose (Ca(2+), 260 s(-1) mM(-1)). There is potential for the enzyme to add value to industrial saccharification operations at low substrate and high d-glucose and high d-xylose concentrations.
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Affiliation(s)
- Douglas B Jordan
- USDA-ARS-National Center for Agricultural Utilization Research, Peoria, IL 61604, USA.
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